Allotropy

Added

- Add parser structure documentation

Changed

- Refactor Agilent Gen5 with explicit dataclasses structure
- Update Benchman Vi-cell Blu adapter to use the new cell-counting BENCHLING/2023/11 schema
- Update Benchman Vi-cell XR adapter to use the new cell-counting BENCHLING/2023/11 schema
- Set mypy's disallow_any_generics to True. Ideally, new files should not suppress these warnings
- Refactor way to extract and validate information from pandas series in AppBio QuantStudio
- Simplify CSV lines reader
- Update PerkinElmer EnVision adapter to use the new plate-reader BENCHLING/2023/09 schema
- Standaradize and clarify exception messages

Added

- Add data system document to plate reader schema

Changed

- Redefine reporter dye setting for genotyping experiments in AppBio QuantStudio
- Refactor Moldev Softmax Pro with explicit dataclasses structure
- Inline VendorParser.parse_timestamp (was only used by VendorParser.get_date_time)
- Change TimeStampParser.parse() to raise for invalid input

Added

- Add missing example outputs for AppBio Quantstudio tests
- Add cell-counting REC/2023/09 schema, with additions to support existing use cases

Fixed

- Update plate-reader schema to be compatible with current supported adapters and change REC -> BENCHLING

Added

- Allow lines reader to accept or infer encoding

Fixed

- Use fuzzy=True for timestamp parsing to handle non-standard cases (e.g. mixing 24h time and AM/PM)

Added

- Governance document
- Added plate-reader REC/2023/09 schema (not in use by parsers yet)

Fixed

Changed

- Relax TimestampParser to use tzinfo for typing
- Change the cell counter schema name to match with the one published by Allotrope (cell counting)
- Update README, CONTRIBUTING, and pyproject.toml
- Rename to PerkinElmerEnvisionParser and RocheCedexBiohtParser for consistency
- Add additional plate reader testing data for the plate reader parser
- Change generic Exceptions to AllotropyErrors

Added

- Test for broken calculated document structure in AppBio QuantStudio

Fixed

- Fix bug in result caching in AppBio Quantstudio

Changed

- Allow block type to have plate well count in any position for AppBio QuantStudio
- Replace datetime.timezone with ZoneInfo in TimestampParser
- Implement CsvReader as child of LinesReader